Mark,
without prior knowledge of what you do, I can just recommend you the recon-all option "-notal-check". You can find out more about it by running "recon-all -help | less".
So your command would look like:
recon-all -autorecon1 -notal-check -s $YOURRAT
Best,
Martin
On Monday 13 October 2008 12:29:52 Mark Bouts wrote:
Hi,
I'm trying to create a template model for rats. I've learned through the surface registration template (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) that I have to run the recon-all procedure at least once. However when I run the recon-all -autorecon1 option it stops at the the talairach detection after completing the talairach_avi. With the message:
Talairach Failure Detection
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
I read through different messages on the mailing list that I had to check the nu.mgz file with tkmedit. This file looks ok considering the fact that a rat brain is considerably smaller.
So my question I like to ask is: how to continue? What could I try?
Is there a template available or does anyone have experience with creating a template for a rat?
Thanks!
Mark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer